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Finite-Size Conformational Transitions: A Unifying Concept Underlying Chromosome Dynamics

Communications in Theoretical Physics 2014年第10期61卷 607-616页

作者： Bertrand R.Caré Pascal Carrivain Thierry Forné Jean-Marc Victor annick lesne Laboratoire de Physique Théorique de la Matière Condensée CNRS UMR 7600UPMC University Paris 06F-75005ParisFrance CNRS GDR 3536 UPMC University Paris 06F-75005ParisFrance Institut de Génétique Humaine CNRS UPR 1142 MontpellierFrance Institut de Génétique Moléculaire de Montpellier CNRS UMR 5535University of MontpellierMontpellierFrance Kavli Institute for Theoretical Physics China CAS

Investigating average thermodynamic quantities is not sufficient to understand conformational transitions of a finite-size polymer. We propose that such transitions are better described in terms of the probability distribution of some finite-size order parameter, and the evolution of this distribution as a control parameter varies. We demonstrate this claim for the coil-globule transition of a linear polymer and its mapping onto a two-state model. In a biological context, polymer models delineate the physical constraints experienced by the genome at different levels of organization,from DNA to chromatin to chromosome. We apply our finite-size approach to the formation of plectonemes in a DNA segment submitted to an applied torque and the ensuing helix-coil transition that can be numerically observed, with a coexistence of the helix and coil states in a range of parameters. Polymer models are also essential to analyze recent in vivo experiments providing the frequency of pairwise contacts between genomic loci. The probability distribution of these contacts yields quantitative information on the conformational fluctuations of chromosome regions. The changes observed in the shape of the distribution when the cell type or the physiological conditions vary may reveal an epigenetic modulation of the conformational constraints experienced by the chromosomes.

关键词： coil-globule transition helix-coil transition chromosome conformational capture two-state model

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CDS:A Fold-change Based Statistical Test for Concomitant Identification of Distinctness and Similarity in Gene Expression Analysis

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Genomics,Proteomics & Bioinformatics 2012年第3期10卷 127-135页

作者： Nicolas Tchitchek José Felipe Golib Dzib Brice Targat Sebastian Noth Arndt Benecke annick lesne Institut des Hautes Etudes Scientifiques Bures-sur-Yvette 91440France Centre National de la Recherche Scientifique USR3078Bures-sur-Yvette 91440France Laboratoire de Physique Théorique de la Matière Condensée CNRS UMR7600Université Pierre et Marie Curie-Paris 6Paris 75005France

The problem of identifying differential activity such as in gene expression is a major defeat in biostatistics and *** important,however much less frequently studied,is the question of similar activity from one biological condition to *** foldchange,or ratio,is usually considered a relevant criterion for stating difference and similarity between ***,no statistical method for concomitant evaluation of similarity and distinctness currently exists for biological *** microarray,digital PCR(dPCR),and Next-Generation Sequencing(NGS) technologies frequently provide a means of coefficient of variation estimation for individual *** fold-change,and by making the assumption that measurements are normally distributed with known variances,we designed a novel statistical test that allows us to detect concomitantly,thus using the same formalism,differentially and similarly expressed genes(http://***).Given two sets of gene measurements in different biological conditions,the probabilities of making type I and type II errors in stating that a gene is differentially or similarly expressed from one condition to the other can be ***,a confidence interval for the fold-change can be ***,we demonstrate that the assumption of normality can be relaxed to consider arbitrary distributions *** Concomitant evaluation of Distinctness and Similarity(CDS) statistical test correctly estimates similarities and differences between measurements of gene *** implementation,being time and memory efficient,allows the use of the CDS test in high-throughput data analysis such as microarray,dPCR,and NGS ***,the CDS test can be applied to the comparison of single measurements(N:1) provided the variance(or coefficient of variation) of the signals is known,making CDS a valuable tool also in biomedical analysis where typically a single measurement per

关键词： Statistical test Fold-change Distinctness Similarity Gene expression Single measurement Patient study

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Fractal Analysis of Lineaments in Equatorial Africa: Insights on Lithospheric Structure

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Open Journal of Geology 2013年第3期3卷 157-168页

作者： Collin Nkono Olivier Féménias annick lesne Jean-Claude Mercier Daniel Demaiffe Isotopic Geochemistry and Chemical Geodynamics Laboratory DSTE (CP 160/02) Université Libre de Bruxelles (ULB) Bruxelles Belgique

In this paper, the complexity in the spatial distribution of the lineaments was investigated from on remote sensing topographic (SRTM DEM) and multispectral (Landsat) data. Lineaments in equatorial Africa were chosen to apply the fractal analysis methodology. The good correlations of the obtained data with some geophysical data from the same area allow that the complexity in the spatial distribution of the lineaments can give qualitative information on the interior of the earth (or on other planets). This method can provide a bridge between classical geology and geophysics, and particularly powerful for studying large and inaccessible regions.

关键词： Lineament Fractal Analysis SRTM Equatorial Africa

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